I'm extremely new to Perl / MySQL / Linux (Ubuntu), so there is every chance that I'm doing something ridiculous. Any help would be greatly appreciated. If i'm asking in the wrong place, sorry.

I'm trying to install a sequence database using the installDBRNASEQ.pl script which is part of a large pipeline called GENE-counter (used to analyse transcriptomic data). I have set up a MySQL database, I can log in and out without any problems, but when I run the command below from the appropriate folder location (-n, -v, variables aren't important, -i is the input file location, -d is the mysql database, -f is required by the script itself)

I'm not sure I expect that to work however as I'm running everything through Perl here. I can run another terminal window, connect to the relevant MySQL database etc., but I don't know how to specify a password and connect to the database using the above command?

Any thoughts /comments would be greatly appeciated. If anyone is willing to help I can post more info as needed.

thanks for the reply. I think I've got to the root problem (in the last few minutes actually) which relates to a change in syntax from TYPE=MyISAM, to ENGINE=MyISAM in one of the associated Perl scripts which connects data to the mysql database. The latest MySQL update changed the syntax and I guess some Perl scripts must be lagging behind.